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Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

99.9%

Charge Balance

100.0%

Metabolite Connectivity

100.0%

Unbounded Flux In Default Medium

100.0%

Sub Total

100%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{99.90 + (4 \cdot 100) +}{(5 \cdot 100)} = 99.99$ $(99.90 + (4 * 100) + )/((5 * 100)) = 99.99$

Annotation - Metabolites

Presence of Metabolite Annotation

100.0%

Metabolite Annotations Per Database

pubchem.compound

0.1%

kegg.compound

86.1%

seed.compound

50.8%

inchikey

0.0%

inchi

0.0%

chebi

82.6%

hmdb

43.0%

reactome

0.0%

metanetx.chemical

82.4%

bigg.metabolite

52.2%

biocyc

50.1%

Metabolite Annotation Conformity Per Database

pubchem.compound

100.0%

kegg.compound

100.0%

seed.compound

100.0%

inchikey

0.0%

inchi

0.0%

chebi

100.0%

hmdb

100.0%

reactome

0.0%

metanetx.chemical

100.0%

bigg.metabolite

100.0%

biocyc

100.0%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

78%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{0.12 + 86.08 + 50.81 + 82.60 + 43.04 + 82.37 + 52.20 + 50.12 + (10 \cdot 100) + (6 \cdot 0)}{(24 \cdot 100)} = 78.35$ $(0.12 + 86.08 + 50.81 + 82.60 + 43.04 + 82.37 + 52.20 + 50.12 + (10 * 100) + (6 * 0))/((24 * 100)) = 78.35$

Annotation - Reactions

Presence of Reaction Annotation

99.9%

Reaction Annotations Per Database

rhea

53.3%

kegg.reaction

69.8%

seed.reaction

5.0%

metanetx.reaction

68.9%

bigg.reaction

3.4%

reactome

0.0%

ec-code

70.2%

brenda

0.0%

biocyc

1.9%

Reaction Annotation Conformity Per Database

rhea

100.0%

kegg.reaction

100.0%

seed.reaction

100.0%

metanetx.reaction

100.0%

bigg.reaction

100.0%

reactome

0.0%

ec-code

99.9%

brenda

0.0%

biocyc

100.0%

Uniform Reaction Identifier Namespace

100.0%

Sub Total

77%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{99.91 + 53.33 + 69.83 + 4.97 + 68.94 + 3.37 + 70.19 + 1.86 + 99.91 + (7 \cdot 100) + (4 \cdot 0)}{(20 \cdot 100)} = 76.99$ $(99.91 + 53.33 + 69.83 + 4.97 + 68.94 + 3.37 + 70.19 + 1.86 + 99.91 + (7 * 100) + (4 * 0))/((20 * 100)) = 76.99$

Annotation - Genes

Presence of Gene Annotation

100.0%

Gene Annotations Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

0.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

33%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(1 \cdot 100) + (20 \cdot 0)}{(21 \cdot 100)} = 33.33$ $((1 * 100) + (20 * 0))/((21 * 100)) = 33.33$

Annotation - SBO Terms

Metabolite General SBO Presence

95.7%

Metabolite SBO:0000247 Presence

92.5%

Reaction General SBO Presence

99.9%

Metabolic Reaction SBO:0000176 Presence

99.7%

Transport Reaction SBO:0000185 Presence

98.1%

Exchange Reaction SBO:0000627 Presence

100.0%

Demand Reaction SBO:0000628 Presence

Skipped

Sink Reactions SBO:0000632 Presence

Skipped

Gene General SBO Presence

100.0%

Gene SBO:0000243 Presence

100.0%

Biomass Reactions SBO:0000629 Presence

50.0%

Sub Total

76%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{95.71 + 92.46 + 99.91 + 99.68 + 98.10 + 50.00 + (3 \cdot 100) + (2 \cdot 0)}{(11 \cdot 100)} = 75.99$ $(95.71 + 92.46 + 99.91 + 99.68 + 98.10 + 50.00 + (3 * 100) + (2 * 0))/((11 * 100)) = 75.99$

Total Score

83%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 99.99) + (1 \cdot 78.35) + (1 \cdot 76.99) + (1 \cdot 33.33) + (2 \cdot 75.99)}{(3 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (2 \cdot 100)} = 83.20$ $((3 * 99.99) + (1 * 78.35) + (1 * 76.99) + (1 * 33.33) + (2 * 75.99))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 83.20$

Total Score

83%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

FBC enabled

Errored

Basic Information

Model Identifier

GTModelBeata2015

Total Metabolites

862

Total Reactions

1,127

Total Genes

760

Total Compartments

Metabolic Coverage

1.48

Metabolite Information

Unique Metabolites

786

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

941

Purely Metabolic Reactions with Constraints

Transport Reactions

105

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

0.34

Reactions With Partially Identical Annotations

0.01

Duplicate Reactions

0.00

Reactions With Identical Genes

0.50

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

197

Fraction of Transport Reactions without GPR

1.00

Enzyme Complexes

Biomass

Biomass Reactions Identified

Biomass Consistency

BIOMASSt

0.00

biomass

0.75

Biomass Production In Default Medium

BIOMASSt

0.70

biomass

0.70

Unrealistic Growth Rate In Default Medium

BIOMASSt

false

biomass

false

Biomass Production In Complete Medium

BIOMASSt

43.22

biomass

43.22

Blocked Biomass Precursors In Default Medium

BIOMASSt

biomass

Blocked Biomass Precursors In Complete Medium

BIOMASSt

biomass

Ratio of Direct Metabolites in Biomass Reaction

BIOMASSt

0.00

biomass

0.05

Number of Missing Essential Biomass Precursors

BIOMASSt

biomass

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

BIOMASSt

false

biomass

true

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

212

Universally blocked reactions are reactions that during Flux Variability Analysis cannot carry any flux while all model boundaries are open. Generally blocked reactions are caused by network gaps, which can be attributed to scope or knowledge gaps. Implementation: Use flux variability analysis (FVA) implemented in cobra.flux_analysis.find_blocked_reactions with open_exchanges=True. Please refer to the cobrapy documentation for more information: https://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/ variability/index.html#cobra.flux_analysis.variability. find_blocked_reactions

There are 212 (18.81%) blocked reactions in the model: HYDA, PPBNGS, HMBS, ADMDC, GTHPi, ...

["HYDA","PPBNGS","HMBS","ADMDC","GTHPi","FCLT","UAG2EMA","AAGAMPT","UAG2E","UAGCVT","ORNAT","HOPNTAL","F6PCPT","F6PUPT","F6PIPT","NO2R","CAT23DOX","ALASm","G3PCT","SBTD_D2","MMSAD1","PPCOAOm","ACACT10m","GLGC","2HBO","URAHL","GGGH","NDPK8","ALAALAr","BNOR","BTCOAOR","ACACT2","DGALIGH","ACOAD7f","AACOAT","HMGCOALY","UGE","MTAN","DHBS","DHBD","UAGUDPGPTRANS","FTHFLIG","ARABINANHY","FBA4","XYLUPT","SPMS","HIBDm","PGAMT","NDPK4","DTMPK","QH2NOR","G1SAT","PYNP1","FOMETRi","FTCL","NDPK7","NDPK6","OP4ENLY","OXALCCLY","HMCNSADLY","GAMPT","MNLPT","ACMANAHY","PUNP6","HMSD","TREPT","UAMAGS","UAAGDS","ASAPT","MELTGH","ICHORT","MERCPPYRST","UPP3S","CYANST","UACCGOR","UAPGR","UAMAS","UPP3MT","UPPDC1","PPPGO_1","UACMAMO","ALCD4","ALCD4y","TOL2OR","CRESOLOR","SLNTOR","ACOAD3f","ACACT4m","ACOAD5f","ACACT6m","PC20M","4OT","ACOAD6f","ACACT7m","SMBCOAOR","GLUTRR","MTRK","NNDMBRT","ECOAH5","HACD9","ECOAH9ir","ADPT2","SALCNPT","MHPGLUT","MTRI","MDRPD","23DK5MPPISO","2OH3K5MPPISO","ACDO","RZ5PP","UGMDDS","HACD7","ECOAH7","HACD6","ECOAH6","HACD5","ACACT5r_1","HACD4","ECOAH4","HACD3","ECOAH3","HEXACOAT","HACD2","ECOAH2","ACOAD2f","ACOAD4f","SELMELY","SELCYSTL","UPP1S","UPPDC2","UAGPT3","ARBTPT","AB6PGH","SALCN6PH","PC6YM","PC6AR","PC8XM","PC17M","PC11M","PRE3AOR","CO1DAMT","ADOCBIK","ACBIPGT","ADOCBLS","HGBYR","ACDAH","P6AS","COCHL","CYRDAR2","ACCOAT","FRDPT","GLUTRS","DTPCUDCPPPH","PAPPT3","FMNRx","FLDO","CHLACOR","NODOx","NODOy","SUCHY","CELLBHY","UAAAGGLAAT","FRDPPT","ADCPS2","THRPD","ADOCBIP","XU5PGT","S7PTRANSPP","CPPPGO2","AMETTRANS","AHCYSMETTRANS","ADOCBITRANS","DECDPPP","ADCPS1","ARAT","HEMEOS","CHOLD","IPDPCT","CCTTPENPP","DTPCHEXPPCT","DTPCHEPPCT","DTPCOCPPCT","DTPCNOPPCT","ACGAMT","SELHCYSMT","COBALT2tabc","EX_cl_e","EX_cobalt2_e","EX_arbt_e","EX_salcn_e","LALDO2x","GSPMDS","B23DONOR","ACTD","ACTNAT","ACEDIA","CLt","ARBTtpts","SALCNtpts","RMNt","RMI","RMK","RMPA","EX_rmn_e","FORt","LTHRK","SELR","SELtabc","EX_sel_e","BETALDHx","BETALDHy","ACCR"]

Orphan Metabolites

Dead-end Metabolites

Dead-ends are metabolites that can only be produced but not consumed by reactions in the model. They may indicate the presence of network and knowledge gaps. Implementation: Find dead-end metabolites structurally by considering only reaction equations and reversibility. FBA is not carried out.

A total of 31 (3.60%) metabolites are not consumed by any reaction of the model: adocbl_c, tcynt_c, psuri5p_c, 1pyr5c_c, thpglu_c, ...

Stoichiometrically Balanced Cycles

203

Metabolite Production In Complete Medium

235

Metabolite Consumption In Complete Medium

294

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

Rank

840

Degrees Of Freedom

287

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.10

Platform Linux

Memote Version 0.10.2

Package Versions